Ecological Archives E094-084-D1

D. A. Kelt, P. L. Meserve, J. R. Gutiérrez, W. Bryan Milstead, M. A. Previtali. 2013. Long-term monitoring of mammals in the face of biotic and abiotic influences at a semiarid site in north-central Chile. Ecology 94:977. http://dx.doi.org/10.1890/12-1811.1


Small Mammal Metadata

Introduction

Our long-term research program was established in 1989 to evaluate the relative role of competition and predation in structuring small mammal assemblages, as well as cascading effects on the plant community. In the 3rd and 4th years of this study our site experienced an El Niño / Southern Oscillation (ENSO) warm (high rainfall) event which resulted in a near-doubling of the annual rain (233 and 229 mm in 1991 and 1992, respectfully; the long-term mean from 1989 to 2005 was 139.4 mm). Another ENSO warm event occurred in 1997, and a prolonged one in 2000–2002. Reflecting our developing recognition of the priority of abiotic influences at this site the focus of our research transitioned to one of the relative importance of biotic (predation, competition) and abiotic (rainfall) influences on biotic composition and functioning. In recent years we have begun to focus on long-term stability and dynamics of the biotic assemblage at our site in the face of likely climate change. This metadata file outlines our field methods and the structure of the small mammal data set.

Metadata

Class I. Data set descriptors

A. Data set identity: Long-term monitoring in the face of biotic and abiotic influences at a semiarid site in north-central Chile.

B. Data set identification code:

Fray_Jorge_Small_Mammals_19890-200512.txt

C. Data set description

Current Principal Investigators:

Douglas A. Kelt, Department of Wildlife, Fish, & Conservation Biology, University of California, Davis, CA 95616 USA

Peter L. Meserve, Department of Biological Sciences, Northern Illinois University, DeKalb, IL 60115 USA

Julio R. Gutiérrez, Departamento de Biología, Universidad de La Serena, La Serena, Chile

Abstract: The data set covers a 16-year period (1989–2005) of monthly surveys of small mammal. The small mammal fauna is trapped every month on all experimental plots and information on each captured small mammal is contained in this file. These data have been applied to diverse population- and community-level analyses and remain useful for investigations of population dynamics, species interactions, and the relative influence of biotic and abiotic influences. Sampling is ongoing and data will be added over time.

D. Key words: climate; competition; LTREB data; population dynamics; predation; semiarid ecosystem; small mammals; species interactions.

Class II. Research origin descriptors

A. Overall project description

Identity: Capture data for every small mammal caught in our study site in the Quebrada de Las Vacas located in Bosque Fray Jorge National Park, IV Region, Chile.

Originators: See main metadata file metadata.php.

Period of Study: 1989–2005, ongoing.

Objectives: To monitor the community- and population-level dynamics of semiarid-zone small mammals and characterize the influence of competition, predation, and rainfall on small mammal assemblage structure and composition, and cascading influences on vegetative structure and composition.

Sources of funding: See main metadata file metadata.php.

B. Specific subproject description

1. Site description: See main metadata file metadata.php.

2. Experimental/Sampling design: See main metadata file metadata.php.

Treatments: See main metadata file metadata.php., Table 1, for details on treatment assignments for each plot.

Data Collection Period, Frequency: Small mammals are trapped for four days/month/grid (5 × 5 stations, 15-m interval, two traps/station). As noted in the Master Metadata File, degus (Octodon degus) are removed from degu exclusion plots (e.g., “-D-P” and “-D+P” treatments), and all small mammals are removed from small mammal exclusion plots (“-SM”).

3. Research Methods

Field: We have a small house on site, and our field crew lives there for nine days every month (second–tenth day of the month). They trap eight grids for four nights followed by the other eight grids for four nights (from 1997–2002 the crew added two +F grids to each 4-d cycle). Two Sherman-type live traps (9 × 11 × 30 cm) are placed at each station (hence, 50 traps per grid) and checked 2–3 times daily (morning, late afternoon, midday under hot conditions). All individual small mammals are uniquely marked with numbered ear tags or leg bands (National Band and Tag Co., Newport, Kentucky, USA), and standard data are recorded (see Table 1). Because our site experiences fog or high clouds frequently, we do not target sampling to a particular lunar phase.

Taxonomy and systematics: Taxonomy of small mammals is consistent with the third edition of Mammal Species of the World (Wilson and Reeder 2005) with the minor exception that Abrocoma bennetti is mis-spelled therein as Abrocoma bennettii (although the epithet is spelled correctly in the Index).

4. Project personnel: The field crew includes four technicians; over the years we have supported 27 technicians, some in excess of 10 years on the project. Additionally, the crew frequently recruits volunteers to assist with monthly surveys.

 

Class III. DATA SET STATUS AND ACCESSIBILITY

A. Status

Latest Update: December 2005.

Latest Archive date: December 2005.

Metadata status: The metadata are complete and up to date.

Data verification: Reflecting the complexity of our data set, data verification is a lengthy and iterative procedure.

Definitions:

Record

Line of data.

Master Capture Table

File containing data for all records through the history of the project.

CaptureID

A sequential and unique number assigned to each capture record when entered to the Master Capture Table.

Tag

Refers to uniquely numbered identifiers applied to small mammals. These include ear tags, leg bands, and Michel tags (surgical clips).

AnimalID

A unique number that corresponds to the most recent tag applied to the animal. AnimalIDs are updated through the Master Capture Table whenever tags are replaced.

Identification Change Table

File containing records of all tag changes. The Identification Change Table is not included in this Data Paper.

NewNum

When tags are replaced, this is the new tag number; NewNum becomes the AnimalID throughout the Master Capture Table, until and unless this tag is again replaced.

OldNum

When tags are replaced, this is the old tag number.

Corrections Log

File containing records of all records with data inconsistencies and the corrections made by the data managers (see points 12–14, below). All corrections are referenced to the CaptureID in the Master Capture Table. Corrections Logs are developed for each database update, and are not included in this Data Paper.

Procedures:

1. Field crews record all capture data on standardized field data sheets.
2. Tags are applied by technicians sequentially.
3. Lead technician checks data sheets daily to ensure that writing is legible, that all required information has been included, and that any notes or comments on datasheets are clear and unambiguous.
4. Lead technician enters capture data into a formatted Microsoft Excel spreadsheet.
5. Field data sheets are digitized and saved as PDF files.
6. Data (Excel file) and data sheets (PDF) are uploaded to a secure FTP site accessible to all investigators.
7. Data managers review the data of every new field session upon receipt for general consistency.
a. Each capture record is assigned a sequential and unique number (CaptureID).
b. All data fields are reviewed to ensure they are complete and properly formatted.
c. Fields are sorted or organized with Pivot tables to verify that all data are properly formatted, within range of accepted values, and standard abbreviations and codes are used. Inconsistencies are checked against field data sheets or returned to the lead technician for verification if necessary.
8. Once the data have passed the visual verification they are appended to the project’s Master Capture Table in a Microsoft Access database. This table includes all monthly capture data since the project began in March 1989.
9. We employ 3 types of tags: Leg bands, ear tags, and Michel tags (surgical clips). All bands are sequentially numbered; numbers for leg bands and ear tags are numeric whereas Michel tags have alphanumeric codes which are converted to 6-digit numeric identifications that are different from the other series used.
10. Replacement bands or tags (e.g., animals whose leg bands or ear tags are replaced with both the previous and new numbers known) are recorded in an Identification Change Table within the MS Access database. Hence, our Access database includes two tables of relevance here, the Identification Change Table and the Master Capture Table. Each line of data (record) has a unique CaptureID; all individual animals have an AnimalID which is repeated each time an animal is recaptured; the Identification Change Table cross references all replacement tags with earlier tags on animals, allowing us to track replaced tags over time; when tags are replaced, the AnimalID for that individual will be updated throughout the database to the newest tag number (see 11 below).
11. As a consistency check all records that report multiple tags for an animal (tag changes or animals with 2 tags) are compared to the Identification Change Table to make sure they are included.
The Identification Change Table is then reviewed to make sure that identification changes are appropriately recorded and assigned to the correct (most recent) tag number. Below is an example of the entries of the identification table for an animal that had an old band removed (OldNum) and replaced by a new band on two different occasions, the most recent number (NewNum) is then assigned to all records of this animal in the Master Capture Table. This step involves doing a database query to integrate the capture records to the Identification Change Table and assign each unique animal a unique identification number (AnimalID).


CaptureID

NewNum

OldNum

Comment

34345

28995

23456

23456 replaced with 23987; updated to 28995 after 2nd tag change, below.

38567

28995

23987

23987 replaced with 28995

12. A data consistency check is then performed to make sure that each AnimalID is assigned to a single species and a single sex throughout the Master Capture Table.
  Queries are run to check for AnimalID attributed to multiple species or genders.
b.  AnimalIDs with multiple records for a single trap revision (same day and hour) are also flagged with a query as they are likely errors (at times we have animals that are released and immediately enter a trap at a different station, but this is uncommon).
c.  A list of AnimalIDs with data inconsistencies is generated and all records for these individuals are written to a temporary Microsoft Excel table. This table is sorted by date to see the capture history for each individual with an inconsistency.
13. All records with data inconsistencies are reviewed individually by the data managers.
a.  Most data inconsistencies can be corrected by visual inspection of the data.
i.  For each AnimalID the capture dates, location (grid and trap station), weight, sexual and reproductive state, and ancillary observations are used to verify that the records represent a single individual.
ii.  If the data are consistent with a single individual, logic and majority rule are used to infer the sex and species. That is, we change the record with an inconsistency to the value recorded in the majority of occasions if more than one previous record exists. Records are then updated to reflect the majority decisions.
iii.  When no majority exists (e.g., recorded once as male and once as female) the sex and/or species is set to “unknown” (U or UN respectively); future consistency checks may resolve these. That is, if in a later occasion an AnimalID with a U for the sex is recorded as female then this will be detected during data consistency check and the sex for all the records of this animal will be changed to F.
b.  Data inconsistencies that remain unresolved visually require greater effort. In most cases these inconsistencies result from errors in tag reading or data entry.
i.  These records are reviewed and compared to the original field data sheets to check for data entry errors. It is largely for this purpose that field data sheets are stored as pdf files on a secure ftp server.
ii.  If the AnimalID, sex, species, and revision were entered correctly we check to see if the AnimalID is similar to other animals known to be captured at the location with the same species, sex, sexual, and reproductive state and a similar weight. Common errors such as recording a 7 for a 9, the omission of a leading or trailing number, or reading a number backwards, are corrected and logged in a spreadsheet of the Corrections Log.
iii.  Inconsistencies in the AnimalID that cannot be resolved are left unchanged for several field sessions.
iv.  If these are not resolved within several field sessions the least convincing AnimalID is listed as unresolved by changing the AnimalID to <NULL> and coding the change in the database with a comment (“99”) and the date of the corresponding Corrections Log. These records are removed from future analysis of the data.
14.  A log of all changes (Corrections Log) is kept. This includes the original data inconsistencies in the records and the correction or change is recorded in a Change Comments field. The Master Capture Table is then updated by incorporating the change to the appropriate record based on the CaptureID, and adding a code in the comments indicating a change had been made and where to find the details in the Corrections Log (i.e., name of the specific Log and the date of the data revision). Currently the Corrections Logs are kept in a set of Microsoft Excel files named by the date of the data revision.
15. Tag number series may be reused.Before this occurs the database is checked to assure that no animals from the previous use of the series have been captured within the last 3 years. To avoid confusion, records for the earlier series in the database are identified and modified before records from the reused series are added. The older numbers are modified by the addition of a large number. For example, when the 19,000 series (19,000–19,999) was reused we added 9,000,000 to each number; hence tag 19,123 becomes 9,019,123, and so on. This preserves the number in a recognizable form while ensuring it is still unique.

 

B. Accessibility

Storage location and medium: (Ecological Society of America data archives [Ecological Archives], URL published in each issue of its journals). Original mammal data files reside with Douglas A. Kelt and W. Bryan Milstead, and are archived in a separate server. Original datasheets reside with Julio R. Gutiérrez. Small mammal datasheets also are scanned and stored on a server maintained by W. Bryan Milstead.

Contact person: Douglas A. Kelt, Department of Wildlife, Fish, and Conservation Biology, University of California, Davis CA 95616-5270, USA. Phone: +1 (530) 754-0145 E-mail: dakelt@ucdavis.edu.

Copyright restrictions: None.

Proprietary restrictions: We impose no proprietary restrictions on these data, but we do request that authors pursuing analytical efforts with these data communicate with us in advance to prevent redundant efforts. Additionally, we request that authors of publications using these data notify Douglas A. Kelt (contact information above) of publication of their study. This helps us to document the scientific value and use of these data and will contribute to our annual reporting to the funding agencies.

Costs: None.

 

Class IV. DATA STRUCTURAL DESCRIPTORS

A. Data Set File

Identity: Fray_Jorge_Small_Mammals_198903-200512.txt

Size: 368,759 rows (including header), 17.06 Mb.

Format and storage mode: ASCII text, tab-delimited.

Header information: The first row of the file contains the variable names below.

Alphanumeric attributes: Mixed.

B. Variable information

Table 1. Column information for Fray_Jorge_Small_Mammals_198903-200512.txt. Each row in this data set comprises all data collected for each individual small mammal captured during a survey. Multiple captures of individuals are recorded on separate lines. A period indicates missing data.

Variable name

Variable definition

Variable codes, definitions, and notes

MO

Year and month.

Year and month: e.g., March, 2000 = 200003.

DATE

Julian date, numbered sequentially beginning September 1, 1988.

Integer.

HOUR

Time of trap revision.

0 = Morning;
1 = Regular afternoon revision;
2 = On hot days, a second morning or mid-day revision is added (occurs before Hour = 1);
3 = On a few occasions, a second mid-day revision was added (after Hour = 0 and Hour = 2 but before Hour= 1).

GR

Grid number.

1 to 20

ROW

Trapping Row.

1 to 5;
If row unknown entered as 0.

COL

Trapping Column.

1 to 5;
If col unknown entered as 0

TRT

Treatment

+D -P = Plus Degu Minus Predator
-D -P = Minus Degu Minus Predator
+D +P = Plus Degu Plus Predator
-D +P = Minus Degu Plus Predator
+F = Plus Food
-SM = Minus all Small Mammals (-D-P plots converted to –SM in 2000)

AnimalID

A unique number that corresponds to the most recent tag applied to the animal.

Integer

SP

Species.

See Table 2.

SEX

Gender of animal.

M = Male;
F = Female;
U = Unknown

WT

Weight (Grams).

Integer values (no decimals).
“.” = no data.

SST

Sexual State.

0 = unknown;
1 = imperforate (♀)/ testes not descended (♂);
2 = perforate (♀)/ testes descended (♂).

RST

FEMALE Reproductive State.

0 = non-reproductive or male;
1 = pregnant;
2 = recently or presently lactating;
3 = pregnant and lactating;
“.” = no data

ST

Status of animal

0 = New. Animal not previously captured;
1 = Previously captured and marked;
2 = Remarked. Animal obviously previously marked but tag lost, previous number unknown;
3 = Changed. Animal in danger of losing a tag (ear torn; band tight) so new tag applied. Old tag is recorded and archived;
“.” = no data.

F

Fate of animal

0 = Released;
1 = Died in trap;
2 = Injured in trap or during handling;
3 = Escaped;
4 = Repeated capture (during the same trap check; e.g., 2nd capture on a given morning;
5 = Animal removed from the grid. Release site unknown or different from 6 or 7, below; pertains to -D and –SM grids only;
6 = Animal removed from the grid, released between grids 2 and 3; pertains to -D and –SM grids only;
7 = Animal removed from grid, released between grids 11 and 12; pertains to -D and –SM grids only.

 

Table 2. Species codes employed in Fray_Jorge_Small_Mammals_198903-200512.txt, and general characteristics of these taxa. Codes were established in 1989 and some names have changed (hence, ME for Thylamys elegans, which was Marmosa elegans in 1989).

Code

Species

Common Name

Species Type1

Diet2

Weight in grams (SD)

AB

Abrocoma bennetti

Bennett’s chinchilla rat

Opportunistic

Herb

171 (65)

AL

Abrothrix longipilis

Long-haired akodont

Opportunistic

Insectiv.

47 (9)

AO

Abrothrix olivaceus

Olive-colored akodont

Core

Omniv.

28 (6)

CH

Chelemys megalonyx

Large long-clawed akodont

Rare

Insectiv.

34 (5)

LU

Octodon lunatus

Moon-toothed degu

Rare

Herbiv.

136 (36)

ME

Thylamys [Marmosa] elegans

Elegant fat-tailed mouse opossum

Core

Insectiv.

22 (8)

OD

Octodon degus

Degu

Core

Herbiv.

128(29)

OL

Oligoryzomys longicaudatus

Long-tailed colilargo

Opportunistic

Graniv.

27 (7)

PD

Phyllotis darwini

Darwin’s pericote

Core

Herbiv./ Graniv.

54 (14)

RN

Rattus norvegicus

Norway rat

Rare

Omniv.

128 (44)

RR

Rattus rattus

Black rat

Rare

Omniv.

110 (50)

SC

Spalacopus cyanus

Coruro (fossorial)

Rare?

Herbiv.

80-140g3.

1. Milstead et al. (2007).
2. Meserve (1981).
3. Weight from Muñoz-Pedreros and Gil (2009).

 

Class V. Supplemental descriptors

A. Publications using the data set: See main metadata file metadata.php.

 

Literature cited

Meserve, P. L. 1981. Trophic relationships among small mammals in a Chilean semi arid thorn scrub community. Journal of Mammalogy 62:304–314.

Milstead, W. B., P. L. Meserve, A. Campanella, M. A. Previtali, D. A. Kelt, and J. R. Gutiérrez. 2007. Spatial ecology of small mammals in north-central Chile: role of precipitation and refuges. Journal of Mammalogy 88:1532–1538.

Muñoz-Pedreros, A., and C. Gil. 2009. Orden Rodentia. Pages 93–157 in A. Muñoz-Pedreros and J. Yáñez Valenzuela, editors. Mamíferos de Chile, Second edition. CEA Ediciones, Valdivia, Chile.

Wilson, D. E., and D. M. Reeder. 2005. Mammal species of the world: a taxonomic and geographic reference. Third edition. Johns Hopkins University Press, Baltimore, Maryland, USA.


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